Biology subjects

Dragos, A.

Publications and source records attributed to Dragos, A..

14 recordsLinked to original sources

bioRxiv2026

Chemical inactivation of a bacterial immune system de-domesticates a temperate phage and promotes its spread

Microbial communities shape hosts and ecosystems, yet the behaviors of these microbes are themselves controlled by mobile genetic elements. These mobile genetic elements (MGEs) compete and influence one anothers distributions. For example, many anti-phage immune systems are carried by prophages, plasmids, and integrative and conjugative elements (ICEs). It is unclear how important each of these interference mechanisms is for the spread of different mobile elements. Chemical inhibitors of these mechanisms of inter-MGE competition can clarify their mechanisms and significance in diverse environments. We discovered chemical inhibitors of SpbK--an antiphage defense encoded by an ICE in several strains of Bacillus subtilis. It is believed to prevent the dissemination of SP{beta} -like temperate phages, forcing SP{beta} to remain domesticated in its ICE-containing host. Chemical inhibition of SpbK dramatically improved the escape of infectious SP{beta} phages capable of disseminating and forming new lysogens. Furthermore, SpbK is part of a widespread class of Toll/interleukin-1 receptor (TIR)-domain containing enzymes that are prevalent both in prokaryotic antiphage immune systems and eukaryotic immune signaling. Our inhibitors reveal two distinct mechanisms of inhibiting TIR-domain enzymes. These models of inhibition may broadly apply across immune proteins, enabling inhibition of many TIR immune systems that influence phage spread as well as plant immunity and animal cellular signaling.

biochemistry↗

bioRxiv2026

Resistome and microbiome-immune interactions in an Eastern European population with high antibiotic use

The gut microbiome influences host health, affecting gastrointestinal, metabolic, immune, cardiovascular, and neurological functions. A balanced microbiome is associated with favourable health outcomes. However, excessive antibiotic use and dietary habits can disrupt this ecosystem, leading to dysbiosis and affecting body homeostasis. We present the first comprehensive metagenomic analysis of the gut microbiome in a healthy Romanian cohort. With no prior high-resolution profiling on this population, characterized by high antibiotic consumption, this cohort contributes to understanding microbiome variation in European populations. We report microbiome features consistent with other European populations, including well-defined community configurations, and provide new insights into how these relate to within-phylum diversity. We observe an enrichment of Enterobacteriaceae, a pattern that may be shaped by population-level exposures, including antibiotic use. The analysis of antimicrobial resistance genes, contextualized with data from other cohorts and the European Centre for Disease Prevention and Control, showed an increased prevalence of genes linked to beta-lactams, macrolides, and quinolones--antibiotics commonly used in this population. Finally, we investigate the relationship between the microbial profile and the systemic immune responses, inferred from correlations with in vitro cytokine production. Notably, we identify a potential immune-priming role for Collinsella species and a link between the Prevotella enterotype and the cytokine production capacity. ImportanceThis first comprehensive study of the healthy gut microbiome in a Romanian cohort contributes to a baseline for the microbiome and resistome composition of this population. While universally accepted definitions of "healthy" microbiomes, or baseline resistomes, remain lacking, such data help contextualise future studies and support the monitoring of dynamics. The Enterobacteriaceae abundance suggests a microbiome composition potentially influenced by antimicrobial consumption, a relevant pattern in a region with a high burden of nosocomial infections. In addition, the prevalence of antimicrobial resistance genes, and the concordance with commonly used antibiotics in the community reinforces the need to address antibiotic use in public health strategies. Although links between the gut microbiome and host immunity are not fully understood, our findings are consistent with a role for microbiome composition in immune-related traits. The association between the Prevotella enterotype and cytokine balance may provide a basis for further investigation of enterotype-specific immune characteristics.

microbiology↗

bioRxiv2024

Ecology of prophage-like elements in Bacillus subtilis at global and local geographical scale

Prophages account for a substantial part of most bacterial genomes, but the impacts on hosts remain poorly understood. Here, we combined computational and laboratory experiments to explore the abundance, distribution, and activity of prophage elements in Bacillus subtilis. NCBI database genome sequences and isolates from 1 cm3 riverbank soil samples were analyzed to provide insights at global and local geographical scales, respectively. Most prophages in wild B. subtilis isolates were related to mobile genetic elements previously identified in laboratory strains. Some large groups of prophages were closely related to completely uncharacterized yet functional Bacillus phages, or completely unknown. As certain prophage groups were unique to local isolates, we explored factors influencing prophages within a single genome. Phylogenetic relatedness was a slightly better predictor of host prophage repertoire than geographical origin. We show that cryptic phages can play a major role in acquisition and/or maintenance of other prophage elements both via strong antagonism or by co-dependence. Laboratory experiments showed that most predicted prophages may be cryptic, since they failed to induce under DNA-damaging stress conditions. Interestingly, the magnitude of stress responses remained proportional to the total number of prophage elements predicted, suggesting their importance in host physiology. This study highlights the diversity, integration patterns, and co-occurrence of prophages in B. subtilis and their potential impact on host evolution and physiology. Understanding these dynamics provides insight into bacterial genome evolution and prophage-host interactions, laying the groundwork for future experimental studies on the roles of phages in the ecology and evolution of this bacterial species.

microbiology↗

bioRxiv2021

The Bacillus phage SPβ and its relatives: A temperate phage model system reveals new strains, species, prophage integration loci, conserved proteins and lysogeny management components

The Bacillus phage SP{beta} has been known for about 50 years, but only a few strains are avalible. We isolated four new wild type strains of the SPbeta species. Phage vB_BsuS-Goe14 introduces its prophage into the spoVK locus, previously not observed to be used by SP{beta}-like phages. We could also reveal the SP{beta}-like phage genome replication strategy, the genome packaging mode, and the phage genome opening point. We extracted 55 SP{beta}-like prophages from public Bacillus genomes, thereby discovering three more integration loci and one additional type of integrase. The identified prophages resembled four new species clusters and three species orphans in the genus Spbetavirus. The determined core proteome of all SP{beta}-like prophages consists of 38 proteins. The integration cassette proved to be not conserved even though present in all strains. It consists of distinct integrases. Analysis of SP{beta} transcriptomes revealed three conserved genes, yopQ, yopR, and yokI, to be transcribed from a dormant prophage. While yopQ and yokI could be deleted from the prophage without activating the prophage, damaging of yopR led to a clear-plaque phenotype. Under the applied laboratory conditions, the yokI mutant showed an elevated virion release implying the YokI protein being a component of the arbitrium system.

microbiology↗

bioRxiv2021

Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions

Trophic interactions play a central role in driving microbial community assembly and function. In gut or soil ecosystems, successful inoculants are always facilitated by efficient colonization, however, the metabolite exchanges between inoculants and resident bacteria are rarely studied, particularly in the rhizosphere. Here, we used bioinformatic, genetic, transcriptomic and metabonomic analyses to uncover syntrophic cooperation between inoculant (Bacillus velezensis SQR9) and plant-beneficial indigenous Pseudomonas stutzeri in the cucumber rhizosphere. We found that the synergistic interaction of these two species is highly environmental dependent, the emergence of syntrophic cooperation was only evident in a static nutrient-rich niche, such as pellicle biofilm in addition to the rhizosphere. Our results identified branched-chain amino acids (BCAAs) biosynthesis pathway involved in syntrophic cooperation when forming coculture biofilms. Assaying the metabolome further demonstrated metabolic facilitation among the bacterial strains. In addition, biofilm matrix components from Bacillus were essential for the interaction. Importantly, the two-species consortium promoted plant growth and helped plants alleviate salt stress. In summary, we propose a mechanism in which synergic interactions between a biocontrol bacterium and a partner species promote plant health.

microbiology↗

bioRxiv2020

Phages weaponize their bacteria with biosynthetic gene clusters

Bacteria produce many different specialized metabolites, which are encoded by biosynthetic gene clusters (BGCs). Despite high industrial relevance owing to broad bioactive potential of these metabolites, their ecological roles remain largely unexplored. We analyze all available genomes for BGCs of phage origin. The BGCs predominantly reside within temperate phages infecting certain commensal and pathogenic bacteria. Nearly all phage BGCs encode bacteriocins, which appear to serve as a strong proxy for phage specificity. Using the gut-associated bacterium Bacillus subtilis, we demonstrate how a temperate phage equips its host with a functional BGC, providing it with a competitive fitness advantage over close relatives. Therefore, certain temperate phages use BGCs to weaponize their bacteria against close relatives, leading to evolutionary benefits from lysogeny to the infected host, and hence, to the phage itself. Our study is a large step towards understanding the natural role of specialized metabolites, as well as mutualistic phage-host relationships.

microbiology↗

bioRxiv2020

Impact of Rap-Phr system abundance on adaptation of Bacillus subtilis

Microbes commonly display great genetic plasticity, which has allowed them to colonize all ecological niches on Earth. Bacillus subtilis is a soil-dwelling organism that can be isolated from a wide variety of environments. An interesting characteristic of this bacterium is its ability to form biofilms that display complex heterogeneity: individual, clonal cells develop diverse phenotypes in response to different environmental conditions within the biofilm. Here, we scrutinized the impact that the number and variety of the Rap-Phr family of regulators and cell-cell communication modules of B. subtilis has on genetic adaptation and evolution. We examine how the Rap family of phosphatase regulators impacts sporulation in diverse niches using a library of single and double rap-phr mutants in competition under 4 distinct growth conditions. Using specific DNA barcodes and whole-genome sequencing, population dynamics were followed, revealing the impact of individual Rap phosphatases and arising mutations on the adaptability of B. subtilis.

microbiology↗

bioRxiv2020

Phage recombination drives evolution of spore-forming Bacilli

Phages are the main source of within-species bacterial diversity and drivers of horizontal gene transfer, but we know little about the mechanisms that drive genetic diversity of these mobile genetic elements (MGEs). Recently, we showed that a sporulation selection regime promotes evolutionary changes within SP{beta} prophage of Bacillus subtilis, leading to direct antagonistic interactions within the population. Herein, we reveal that under a sporulation selection regime, SP{beta} recombines with low copy number phi3Ts phage DNA present within the B. subtilis population. Recombination results in a new prophage occupying a different integration site, as well as the spontaneous release of virulent phage hybrids. Analysis of Bacillus sp. strains suggests that SP{beta} and phi3T belong to a distinct cluster of unusually large phages inserted into sporulation-related genes that are equipped with a spore-related genetic arsenal. Comparison of Bacillus sp. genomes indicates that similar diversification of SP{beta}-like phages takes place in nature. Our work is a stepping stone toward empirical studies on phage evolution, and understanding the eco-evolutionary relationships between bacteria and their phages. By capturing the first steps of new phage evolution, we reveal striking relationship between survival strategy of bacteria and evolution of their phages.

microbiology↗

bioRxiv2019

Privatization of biofilm matrix in structurally heterogeneous biofilms

ABSTRACTThe self-produced biofilm provides beneficial protection for the enclosed cells, but the costly production of matrix components makes producer cells susceptible to cheating by non-producing individuals. Despite detrimental effects of non-producers, biofilms can be heterogeneous, with isogenic non-producers being a natural consequence of phenotypic differentiation processes. For instance, in Bacillus subtilis biofilm cells differ in the two major matrix components production, the amyloid fiber protein TasA and exopolysaccharides (EPS), demonstrating different expression levels of corresponding matrix genes. This raises questions regarding matrix gene expression dynamics during biofilm development and the impact of phenotypic non-producers on biofilm robustness. Here, we show that biofilms are structurally heterogeneous and can be separated into strongly and weakly associated clusters. We reveal that spatiotemporal changes in structural heterogeneity correlate with matrix gene expression, with TasA playing a key role in biofilm integrity and timing of development. We show that the matrix remains partially privatized by the producer subpopulation, where cells tightly stick together even when exposed to shear stress. Our results support previous findings on the existence of ‘weak points’ in seemingly robust biofilms as well as on the key role of linkage proteins in biofilm formation. Furthermore, we provide a starting point for investigating the privatization of common goods within isogenic populations.IMPORTANCE Biofilms are communities of bacteria protected by a self-produced extracellular matrix. The detrimental effects of non-producing individuals on biofilm development raises questions about the dynamics between community members, especially when isogenic non-producers exist within wild-type populations. We asked ourselves whether phenotypic non-producers impact biofilm robustness, and where and when this heterogeneity of matrix gene expression occurs. Based on our results we propose that the matrix remains partly privatized by the producing subpopulation, since producing cells stick together when exposed to shear stress. The important role of linkage proteins in robustness and development of the structurally heterogeneous biofilm provides an entry into studying the privatization of common goods within isogenic populations.Competing Interest StatementThe authors have declared no competing interest.View Full Text

microbiology↗

bioRxiv2019

BiofilmQ, a software tool for quantitative image analysis of microbial biofilm communities

Biofilms are now considered to be the most abundant form of microbial life on Earth, playing critical roles in biogeochemical cycles, agriculture, and health care. Phenotypic and genotypic variations in biofilms generally occur in three-dimensional space and time, and biofilms are therefore often investigated using microscopy. However, the quantitative analysis of microscopy images presents a key obstacle in phenotyping biofilm communities and single-cell heterogeneity inside biofilms. Here, we present BiofilmQ, a comprehensive image cytometry software tool for the automated high-throughput quantification and visualization of 3D and 2D community properties in space and time. Using BiofilmQ does not require prior knowledge of programming or image processing and provides a user-friendly graphical user interface, resulting in editable publication-quality figures. BiofilmQ is designed for handling fluorescence images of any spatially structured microbial community and growth geometry, including microscopic, mesoscopic, macroscopic colonies and aggregates, as well as bacterial biofilms in the context of eukaryotic hosts.

microbiology↗

bioRxiv2018

Cheater-mediated evolution shifts phenotypic heterogeneity in Bacillus subtilis biofilms

Biofilms are closely packed cells held and shielded by extracellular matrix composed of structural proteins and exopolysaccharides (EPS). As matrix components are costly to produce and shared within the population, EPS-deficient cells can act as cheaters by gaining benefits from the cooperative nature of EPS producers. Remarkably, genetically programmed EPS producers can also exhibit phenotypic heterogeneity at single cell level. Previous studies have shown that spatial structure of biofilms limits the spread of cheaters, but the long-term influence of cheating on biofilm evolution is not well understood. Here, we examine the influence of EPS non-producers on evolution of matrix production within the populations of EPS producers in a model biofilm-forming bacterium, Bacillus subtilis. We discovered that general adaptation to biofilm lifestyle leads to an increase in phenotypical heterogeneity of eps expression. Apparently, prolonged exposure to EPS-deficient cheaters, may result in different adaptive strategy, where eps expression increases uniformly within the population. We propose a molecular mechanism behind such adaptive strategy and demonstrate how it can benefit the EPS-producers in the presence of cheaters. This study provides additional insights on how biofilms adapt and respond to stress caused by exploitation in long-term scenario.

microbiology↗

bioRxiv2017

Division of labor during biofilm matrix production

Organisms as simple as bacteria can engage in complex collective actions, such as group motility and fruiting body formation. Some of these actions involve a division of labor, where phenotypically specialized clonal subpopulations, or genetically distinct lineages cooperate with each other by performing complementary tasks. Here, we combine experimental and computational approaches to investigate potential benefits arising from division of labor during biofilm matrix production. We show that both phenotypic and genetic strategies for a division of labor can promote collective biofilm formation in the soil bacterium Bacillus subtilis. In this species, biofilm matrix consists of two major components; EPS and TasA. We observed that clonal groups of B. subtilis phenotypically segregate into three subpopulations composed of matrix non-producers, EPS-producers, and generalists, which produce both EPS and TasA. This incomplete phenotypic specialization was outperformed by a genetic division of labor, where two mutants, engineered as specialists, complemented each other by exchanging EPS and TasA. The relative fitness of the two mutants displayed a negative frequency dependence both in vitro and on plant roots, with strain frequency reaching a stable equilibrium at 30% TasA-producers, corresponding exactly to the population composition where group productivity is maximized. Using individual-based modelling, we show that asymmetries in strain ratio can arise due to differences in the relative benefits that matrix compounds generate for the collective; and that genetic division of labor can be favored when it breaks metabolic constraints associated with the simultaneous production of two matrix components.\n\nHighlights- matrix components EPS and TasA are costly public goods in B. subtilis biofilms\n\n- genetic division of labor using {Delta}eps and {Delta}tasA fosters maximal biofilm productivity\n\n- {Delta}eps and {Delta}tasA cooperation is evolutionary stable in laboratory and ecological systems\n\n- costly metabolic coupling of public goods favors genetic division of labor

microbiology↗

bioRxiv2017

Impaired competence in flagellar mutants of Bacillus subtilis is connected to the regulatory network governed by DegU

The competent state is a developmentally distinct phase, in which bacteria are able to take up and integrate exogenous DNA into their genome. Bacillus subtilis is one of the naturally competent bacterial species and the domesticated laboratory strain 168 is easily transformable. In this study, we report a reduced transformation frequency of B. subtilis mutants lacking functional and structural flagellar components. This includes hag, the gene encoding the flagellin protein forming the filament of the flagellum. We confirm that the observed decrease of the transformation frequency is due to reduced expression of competence genes, particularly of the main competence regulator comK. The impaired competence is due to an increase in the phosphorylated form of the response regulator DegU, which is involved in regulation of both flagellar motility and competence. Altogether, our study identified a close link between motility and natural competence in B. subtilis suggesting that hindrance in motility has great impact on differentiation of this bacterium not restricted only to the transition towards sessile growth stage.\n\nOriginality-Significance statementUnderstanding how versatile bacterial phenotypes influence each other is important for our basic understanding of microbial ecology. Our research highlights the novel intertwinement of bacterial differentiation and reveal how lack of single cell motility adjusts DNA exchange among bacterial strains.

microbiology↗

bioRxiv2017

Evolution of exploitative interactions during diversification in Bacillus subtilis biofilms

Microbial biofilms are tightly packed, heterogeneous structures that serve as arenas for social interactions. Studies on Gram negative models reveal that during evolution in structured environments like biofilms, isogenic populations commonly diversify into phenotypically and genetically distinct variants. These variants can settle in alternative biofilm niches and develop new types of interactions that greatly influence population productivity. Here, we explore the evolutionary diversification of pellicle biofilms of the Gram positive, spore-forming bacterium Bacillus subtilis. We discover that - similarly to other species - B. subtilis diversifies into distinct colony variants. These variants dramatically differ in biofilm formation abilities and expression of biofilm-related genes. In addition, using a quantitative approach, we reveal striking differences in surface complexity and hydrophobicity of the evolved colony types. Interestingly, one of the morphotypes completely lost the ability of independent biofilm formation and evolved to hitchhike with other morphotypes with improved biofilm forming abilities. Genome comparison suggests that major phenotypic transformations between the morphotypes can be triggered by subtle genetic differences. Our work demonstrates how positive complementarity effects and exploitative interactions intertwine during evolutionary diversification in biofilms.

microbiology↗